Quarto introduction

on:
  workflow_dispatch:
  push:
    branches: main
name: Quarto Publish
permissions: 
    contents: write
    pages: write
jobs:
  build-deploy:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository
        uses: actions/checkout@v4 
      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
          version: pre-release
      - uses: r-lib/actions/setup-r@v2
      - uses: r-lib/actions/setup-r-dependencies@v2

      - name: Publish to GitHub Pages (and render)
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          path: quarto-intro.qmd
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

image: alpine:latest

stages:
  - build_image
  - build_site
  - deploy

build docker image:
  stage: build_image
  image: docker:20.10.12-dind
  before_script:
    - docker info
    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
  script:
    - 'docker pull $CI_REGISTRY_IMAGE:latest || true'
    - docker build --cache-from $CI_REGISTRY_IMAGE:latest --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE:latest .
    - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
    - docker push $CI_REGISTRY_IMAGE:latest
  only:
    changes:
      - Dockerfile

build_site:
  stage: build_site
  image: $CI_REGISTRY_IMAGE:latest
  cache:
    key: $CI_JOB_NAME
    paths:
      - _freeze/
      - _site/
  artifacts:
    name: "$CI_JOB_NAME"
    expire_in: 2 days
    paths:
      - _site/
  before_script:
    # https://mastodon.social/@eddelbuettel/111693310455494722
    - |
      Rscript -e "read.dcf('DESCRIPTION', 'Imports') |> 
        tools:::.split_dependencies() |> 
        names() |> 
        setdiff(tools:::.get_standard_package_names()$base) |> 
        install.packages()"
  script:
    - quarto render
  when: always

Deploy to BASV53:
  stage: deploy
  only:
    - main
  dependencies:
    - build_site
  before_script:
    - 'which ssh-agent || ( apk add --update openssh )'
    - eval $(ssh-agent -s)
    - 'which rsync || ( apk add --update rsync )'
    - echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add - > /dev/null
    - mkdir -p ~/.ssh && chmod 700 ~/.ssh
    - 'echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'
  script:
    - rsync -azh -e "ssh -p 8022" --delete --filter 'protect /preview' $CI_PROJECT_DIR/_site/ $SSH_HOST:/var/www/basv53/

FROM rocker/r2u:22.04

RUN  apt-get update && \
  apt-get install -y \
  curl netbase \
  zip git \
  libxml2-dev libcurl4-openssl-dev libmagick++-dev \
  && rm -rf /var/lib/apt/lists/*

RUN install.r tidyverse rmarkdown biobase knitr V8 gt gtextras  ggimage ggrepel ggupset BiocManager && \
  installBioc.r deseq2 apeglm

# from https://quarto.org/docs/get-started/
ARG QUARTO_VERSION="1.6.33"
RUN curl -LO https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb && \
    apt-get update -qq && apt-get -y install \
    ./quarto-${QUARTO_VERSION}-linux-amd64.deb && rm quarto-${QUARTO_VERSION}-linux-amd64.deb \
    && apt autoremove -y && apt clean -y && rm -rf /var/lib/apt/lists/*

project:
  type: website
  pre-render: "echo Let the rendering begin!"
  post-render:
    - "cp -rv posts/images/. _site/posts/images/"
    - "cp -rv posts/videos/. _site/posts/videos/"
    - "Rscript transfer_site.R upload_site"